We are looking for one master with expertise in clinical microbiology or microbiology, including in the laboratory processing of samples for genomic sequencing for a master fellowship

The ONEIDA project is a multidisciplinary inter-institutional project looking for the application of genomics in the context of infectious diseases and host-pathogen interactions.

Within the NGPHYLO project we are looking for one master with bioinformatics skills. We are offering a master fellowship

Description and Objectives

Despite the successful use of antibiotics and vaccination, bacterial infections are still a major cause of morbidity and mortality worldwide. The changing demographics are shifting the attention to older adults where selective pressures may be radically different from those found in children. Several studies showed that bacterial populations are dominated by a few clones. The plasticity of bacterial genomes means that different isolates can carry a distinct array of antibiotic resistance and virulence genes. However, the relationship between carrying a certain gene complement and becoming a successful clone remains elusive. We have documented the bacterial population structure of several pathogens of the genus Streptococcus and found differences between bacteria that are asymptomatically carried and those causing distinct infections in the various age groups. In addition, we identified genes that are unevenly distributed in the bacterial population, potentially explaining the propensity of certain clones for particular hosts or infections. We have also studied the flow of genetic information between bacteria and the factors enhancing or limiting these exchanges and the role of mobile genetic elements in bacterial diversity. We are currently exploring the differences between bacterial populations at the whole-genome level. We are refining existing approaches to handle high throughput sequence (HTS) data and are developing tools for storing and mining this data in a unified platform, integrating information from existing databases. This is reflected in the development of novel bioinformatic tools with a focus on HTS. We hope to get a detailed view of the genetic differences between bacterial clones and to identify candidate genes to explain their different abundance. We are also looking at streptococci causing infections in humans and animals to identify key events allowing the adaptation to different host species and to evaluate the current potential for zoonotic acquisition. Understanding the dynamics and responses of a bacterial population to the multiple selective pressures imposed on it and the key genetic events allowing the differentiation of specific clones will allow us to better predict bacterial pathogen evolution. Our research also produces important epidemiological information allowing us to anticipate the potential benefits of vaccination or guiding the optimal empirical therapy for infections of suspected streptococcal etiology.

Research Areas

Antimicrobial resistance of pathogens belonging to the genus Streptococcus

The investigations on this field have benefited from a close contact with clinical practice and have focused on issues directly relevant to the clinician. Special attention has been given to the epidemiology of antimicrobial resistance at a national level. These data are essential for the preparation of guidelines for empirical therapy as well as for an understanding of the evolution and dissemination of antimicrobial resistance. The evaluation of the in vitro activity of new antimicrobial agents against clinical isolates and the investigation on the possibility of using bacteriophages as alternative prophylactic or therapeutic agents both stem from our interest in new therapeutic approaches.
The use of molecular technologies provides further detail to these analyses by allowing the molecular identification of bacterial clones and their association to known resistance determinants. This affords new insights into the 1) clonality of clinical isolates; 2) the distribution of antimicrobial resistance determinants and 3) the dispersal of clones. The later information will be particularly useful at the health-care center level were outbreak detection can be the basis for the implementation of containment measures. A more fundamental development will be the identification of clones with high epidemicity or particularly virulent for future analyses including our ongoing efforts at characterizing the genetic complement of characterized populations using microarray technologies.
The lab currently works with the following streptococcal species: S. pneumoniae, S. pyogenes, S. agalactiae and streptococci of the Lancefield groups C and G .

New diagnosis of parasitic diseases

The immediate developments in this line of research will follow the recent realization that flow cytometric principles allow the detection of malaria pigment. This finding will be further explored with the development of this application to the diagnosis of malaria and the development of a novel sensitivity test. This method will also be investigated for it’s usefulness as markers of disease severity. Furthermore, this research will be used to address questions on the interactions of hemozoin and its effect on the immune system. Finally, the results of this research may be useful for the understanding and development of novel antimalarial drugs, because hemozoin seems to be the target of several of the most effective antimalarials available today.

Evolution and population biology of bacterial pathogens

Lack of knowledge on the dynamics of pathogenic bacteria population structure and the forces shaping it motivates our research in this area. We are interested in the role of chromosome plasticity in bacterial adaptation, with a special emphasis in gene exchange and mobile genetic elements. Current efforts in the characterization of the bacteriophage (phage) population of Streptococcus pneumoniae addresses the role of phages as bacterial “predators” and their potential influence in the bacterial population structure and bacterial “social” interactions. Simultaneously, their role in bacterial pathogenesis is investigated by testing for the presence of virulence enhancing traits in phage genomes. Another project is focusing on the response of the population of disease causing bacteria to another major selective pressure, i.e., the introduction of a vaccine. Underlying these questions is the fundamental issue of the relationship between colonizing isolates and the ones causing disease. Taking advantage of the detailed information available on colonization isolates in Portugal we are addressing this question by characterizing contemporary disease causing isolates and exploring the relationships between these two populations. The availability of novel genomic technologies allows the survey the gene complement of these two populations and the relative distribution of mobile genetic elements among them. We expect that the use of these technologies will also open new lines of research on the bacterial adaptation to the expression of acquired genes, of particular interest is the change in virulence caused by gene acquisition.

Bioinformatics for Microbiology

The large amounts of data collected for clinically relevant strains require a concerted effort of data management and data analysis techniques. We are addressing these topics by the development of databases of strains for several species as well as developing online databases for novel typing methodologies based on DNA sequences. We are also focusing in the in silico simulation of bacterial populations using known evolutionary models and developing new data analysis techniques to interpret and visualize the effect of mutation and recombination as evolutionary driving forces. The analyses of population genomics using “comparative genomic hybridization” also lead to the development of new methodologies to analyze this kind of data. Finally, a systems biology approach is driving the development of models integrating the bacterial pathogens and its human hosts in an ecological and evolutionary perspective.